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Theory Department

Our aim is to elucidate various chemical, physical and biological processes from the theoretical perspective using mainly computational approaches implemented for high performance computing, as well as theoretical methods that have constant feed-back to experimental IR and NMR spectroscopy. We focus on problems in molecular pharmacology, drug design, chemical informatics, molecular biophysics, soft matter, materials optimization...



Representative Publications

1. E. R. Cruz-Chu, E. Papadopoulou, J. H. Walther, A. Popadic, G. Li, M.Praprotnik,  P. Koumoutsakos. On phonons and water flow enhancement in carbon nanotubes. Nat. Nanotechnol. 12, 1106-1108, 2017.      

2. L. Noč, E. Šest, G. Kapun, F. Ruiz-Zepeda, Y. Binyamin, F. Merzel, I. Jerman. High-solar-absorptance CSP coating characterization and reliability testing with isothermal and cyclic loads for service-life prediction. Energy Environ. Sci. 12, 1679-1694, 2019.      

3. L. Delle Site, M. Praprotnik.  Molecular systems with open boundaries: Theory and Simulation. Phys. Rep. 693, 1-56, 2017.     

4. A. Kežar, L. Kavčič, M. Polák, J. Nováček,I. Gutiérrez-Aguirre, M. Tušek Žnidarič, A. Coll, K. Stare, K. Gruden, M. Ravnikar, D. Pahovnik, E. Žagar, F. Merzel, G. Anderluh, M. Podobnik. Structural basis for the multitasking nature of the potato virus Y coat protein. Sci. Adv. 5, 1-13, 2019.

5. A. Prah, E. Frančišković, J. Mavri, J. Stare. Electrostatics as the Driving Force Behind the Catalytic Function of the Monoamine Oxidase A Enzyme Confirmed by Quantum Computations. ACS Catal. 9, 1231-1240, 2019.

6. J. Borišek,S. Pintar, M. Ogrizek, D. Turk, A. Perdih, M. Novič. A Water-Assisted Catalytic Mechanism in Glycoside Hydrolases Demonstrated on the Staphylococcus aureus AutolysinE. ACS Catal. 8, 4334-4345, 2018.     

7. A. Vižintin, J. Bitenc,A. Kopač Lautar, K. Pirnat, J. Grdadolnik,J. Stare, A. Randon-Vitanova, R. Dominko. Probing electrochemical reactions in organic cathode materials via in operando infrared spectroscopy. Nat. Commun. 9, 1-7, 2018.

8. J. Konc, B. Škrlj, N. Eržen, T. Kunej, G. Li, D. Janežič. GenProBiS: web server for mapping of sequence variants to protein binding sites. Nucleic Acids Res. 45, W253-W259,2017.     

9. J. Grdadolnik,F. Merzel, F. Avbelj. Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes. Proc. Natl. Acad. Sci. U.S.A. 114, 322-327, 2017.     

10. A. Kolarič, T. Germe, M. Hrast, C.E.M Stevenson, D.M. Lawson, N.P. Burton, J. Vörös, A. Maxwell, N. Minovski, M. Anderluh, Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds. Nat. Commun., 12, 150-1-150-13, 2021.

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